Chair of Bioinformatics


    Fall workshop in infection biology 2012 by the University of Würzburg

    Autumn School / Summer School from Oct. 23 to Oct. 26, 2012

    Fall Workshop / Fall School in Infection Biology 2012

    University of Würzburg, Germany

    October 23rd – 26th 2012

    Modern Methods in Infection Biology

    The University of Würzburg is listed amongst the top four German universities in the Life Sciences and has a strong focus on infection biology research (source:funding ranking DFG). Participants will learn about new methods, modern techniques, and cutting edge research. Important new methods in transcriptomics, drug screening, microscopy, and system biology will be discussed and demonstrated.








    Participants will gain insight into important models of infectious diseases and modern research methods, as well as gaining a deeper understanding of specific subject areas.

    Target group/selection criteria:

    Outstanding Bachelor/Master students, in addition to PhD students. Applicants are selected on the basis of motivation and qualification. International applications are welcome, as are applications from outstanding students of the University of Würzburg.

    This workshop presents a major opportunity for networking.


    Certificate of Participation

    Language: English


    Application deadline: Sept 30th, 2012

    Participant limit: 25 students

    For application information please contact Dr. Ulrike Rapp-Galmiche at the following email address: ulrike.rapp-galmiche@uni-wuerzburg.de

    Applications should include:

    • letter of motivation (100 words) specifying focus of interest, reason for participation, and expectations

    • curriculum vitae

    • publications if applicable

    A limited number of student stipends (accomodation, travel) will be available on a competitive basis.

    Lecturers will lead the students through the latest techniques in infection biology including microscopy, RNAomics, system biology and drug screening. The organisms we will focus on include plasmodia, trypanosomes, staphylococci and further eubacteria.



    Software required:

    ActivePerl: http://www.activestate.com/activeperl?gclid=COqw-dfblrMCFYta3godwVwAcQ

    BioPerl: http://bioperl.org/DIST

    Blast: ftp://ftp.ncbi.nih.gov/blast/executables/release/LATEST/



    Workshop New Approaches in Infection Biology

    October 23rd- Professor Dr. Dandekar 


    Location: Seminar room of biochemistry B108/109 

    You find that easily, if you start in the main hall or Foyer of the Biocentre of the University of Würzburg


    If you have the lecture theatres A101 (big one) and A102 (medium one) in your back, you just

    turn right, go up the stairs to biochemistry and follow the signs (“workshop, new approaches in infection biology), then you reach the seminar room in B-section of the building, room B108/109.

    Begin: 9:00

    Equipment: notebooks – these are provided (CIP pool and our seminar room is already used by courses, e.g. F2 Bioinformatics and scientific training for the biology teacher students)

    Introduction: Systems biology of infection – bioinformatical approaches

    Prof. Thomas Dandekar 9:00-10:00

    Part I Genome analysis and annotation 10-11:00

    Prof. Thomas Dandekar (basics and challenges of sequence analysis; Annotation and pathway alignment; Comparative genomics)

    Part II Databanks and Ressources 11-12:30

    Dr. Chunguang Liang (Protecs database, EcoliHub / MetaCyc, COGs etc.)

    Lunch break 12:30-13:30

    Part III Modelling metabolic networks 13:30-15:00

    Astrid Fieselmann (how to do elementary mode analysis; simple examples on Staphylococci from own research)

    Coffee break 15:00-15:30

    Part IV Signalling in infectious biology 15:30-17:00

    Dr. Muhammad Naseem (using Squad, gene expression data, semi-quantitative models)

    Part V Current trends in systems biology in infectious biology

    Prof. Thomas Dandekar 17:00-18:00

    (we will show and discuss current trends in systems biology with a focus on computer-based approaches, what they can and what they can not elucidate)

    Workshop New Approaches in Infection Biology

    October 24th- Dr. Susanne Kramer


    Location: Seminar room of biochemistry, B108/109

    Begin: 9:00

    The African trypanosome: a killer and a survival genius

    This course will introduce you to the unusual biology of the African trypanosome. You will explore three features that largely contribute to the parasites pathogenity (antigenic variation, antibody clearance, resistance to the trypanolytic factor) in teams and you will present your results in a rather non-conventional way (by pantomine).

    9:00-9:45  Introduction lecture to Trypanosomes

    9:45-10:30  Movie (African sleeping sickness)

    10:30-11:00  Coffee break

    11:00-12:30  Reading time / research time for pantomine

    12:30-13:30  lunch break

    13:30-14:30  Current Research in Würzburg trypanosome labs: PhD students report

    14:30-16:30  Team discussions, preparing the pantomine (Coffee break in between)

    16:30-17:30  Pantomine

    Workshop New Approaches in Infection Biology

    October 25th- Dr. Martin Fraunholz


    Location: Lecture Seminar room of biochemistry, B108/109

    Lab Department of Microbiology, Room C235

    • Introduction

      • Phagosomal escape of Staphylococcus aureus

      • Principles of Confocal Laser Scanning Microscopy

    • Image analysis of fluorescent micrographs and other imaging data using ImageJ/Fiji

      • images: visualization and manipulation (Background subtraction, Brightness & Contrast)

      • particle counting

      • multi-dimensional images

      • Images stacks and stack manipulation (Aligning stacks slices, measuring intensities over time)

      • Image Montages

    • Experimental part: Phagosomal escape of S. aureus (on a Leica TCS SP5, Room C235; smaller groups)

    Students can bring their own laptops and do image analysis with their own data as well.



    Station 1: PD Dr. Gabriele Pradel

    Confocal laser scanning microscopy: Imaging targets of transmission blocking vaccines.

    Station 2: Ludmilla Sologub

    Giemsa staining: Identifying P. falciparum blood stages in blood smears.

    Station 3: Dr. Matthias Scheuermayer

    Insectary: Dissecting Anopheles stephensi mosquitoes.

    Station 4: Selina Kern

    Malstat assay: Screening drugs in the P. falciparum blood stages.

    Station 5: Andreas von Bohl

    Exflagellation inhibition assay: Evaluating the effect of drugs on gametogenesis.